Journal article
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes
Molecular biology and evolution, v 33(1), pp 13-24
Jan 2016
PMID: 26500251
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.
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Details
- Title
- Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes
- Creators
- Richard C Edmunds - University of OregonBaofeng Su - Auburn UniversityJames P Balhoff - National Evolutionary Synthesis CenterB Frank Eames - University of SaskatchewanWasila M Dahdul - National Evolutionary Synthesis CenterHilmar Lapp - National Evolutionary Synthesis CenterJohn G Lundberg - Drexel UniversityTodd J Vision - National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of North Carolina, Chapel HillRex A Dunham - Auburn UniversityPaula M Mabee - University of South DakotaMonte Westerfield - University of Oregon
- Publication Details
- Molecular biology and evolution, v 33(1), pp 13-24
- Publisher
- Oxford University Press
- Grant note
- P41 HG002659 / NHGRI NIH HHS HD22486 / NICHD NIH HHS U41 HG002659 / NHGRI NIH HHS P01 HD022486 / NICHD NIH HHS HG002659 / NHGRI NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Academy of Natural Sciences of Drexel University
- Web of Science ID
- WOS:000369992600002
- Scopus ID
- 2-s2.0-84964789485
- Other Identifier
- 991019335317604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Evolutionary Biology
- Genetics & Heredity